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Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 January 2024) | Viewed by 10820

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Prof. Dr. Bo Sun

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Guest Editor

College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
Interests: brassica vegetables; Chinese kale; mustard; carotenoids; glucosinolate; antioxidants; nutritional quality; postharvest
Special Issues, Collections and Topics in MDPI journals

Dr. Pengxiang Fan

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Guest Editor

College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
Interests: evolution of plant metabolic network; metabolic network reconstruction; biosynthesis of specialized metabolites; regulation of plant metabolism; plant-herbivore interaction; solanaceae; glandular trichome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Horticultural plants are intensively cultivated crops with high economic value, such as tree fruits, vegetables, ornamental plants, and tea crops. The wide taxonomic distribution and sophisticated domestication history of horticultural crops have led to their highly diverse and complex genomes, which has caused challenges regarding the systematic studies of these plants.

Molecular biology reveals the molecular basis of biological processes in cells, and it is essential for understanding the mechanisms of the execution and regulation of biological processes. Molecular biology technologies have been applied to a wide range of living organisms. However, knowledge about horticultural crops is relatively less available than that on model plants. Recent advances in molecular biology—represented by revolutionary biotechnologies such as plant genome editing and next-generation sequencing—provide unprecedented opportunities to gain insight into the less well-studied horticultural crops.

For this Special Issue, we welcome any original research articles, reviews, short notes, or opinion articles that highlight horticultural crop improvement applications in molecular biology, such as whole-genome resequencing, transcriptomics, proteomics, metabolomics, and genome editing. The topics include, but are not limited to, studies of regulatory mechanisms of plant growth and development, as well as efforts to improve crop yield, quality, and resistance to biotic/abiotic stresses.

Prof. Dr. Bo Sun
Dr. Pengxiang Fan
Guest Editors

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Keywords

horticultural plants
whole-genome resequencing
transcriptomics
proteomics
metabolomics
gene editing
gene regulation
growth and development
yield
quality
resistance

Published Papers (10 papers)

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Research

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17 pages, 42964 KiB

Open AccessArticle

Transcriptomic and Proteomic Analyses Unveil the Role of Nitrogen Metabolism in the Formation of Chinese Cabbage Petiole Spot

by Ying Mei, Juanli Lei, Wenqi Liu, Zhichen Yue, Qizan Hu, Peng Tao, Biyuan Li and Yanting Zhao

Int. J. Mol. Sci. 2024, 25(3), 1366; https://doi.org/10.3390/ijms25031366 - 23 Jan 2024

Viewed by 655

Abstract

Chinese cabbage is the most widely consumed vegetable crop due to its high nutritional value and rock-bottom price. Notably, the presence of the physiological disease petiole spot significantly impacts the appearance quality and marketability of Chinese cabbage. It is well known that excessive nitrogen fertilizer is a crucial factor in the occurrence of petiole spots; however, the mechanism by which excessive nitrogen triggers the formation of petiole spots is not yet clear. In this study, we found that petiole spots initially gather in the intercellular or extracellular regions, then gradually extend into intracellular regions, and finally affect adjacent cells, accompanied by cell death. Transcriptomic and proteomic as well as physiology analyses revealed that the genes/proteins involved in nitrogen metabolism exhibited different expression patterns in resistant and susceptible Chinese cabbage lines. The resistant Chinese cabbage line has high assimilation ability of NH₄⁺, whereas the susceptible one accumulates excessive NH₄⁺, thus inducing a burst of reactive oxygen species (ROS). These results introduce a novel perspective to the investigation of petiole spot induced by the nitrogen metabolism pathway, offering a theoretical foundation for the development of resistant strains in the control of petiole spot. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0)

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21 pages, 10030 KiB

Open AccessArticle

Comprehensive Analysis of NAC Transcription Factors Reveals Their Evolution in Malvales and Functional Characterization of AsNAC019 and AsNAC098 in Aquilaria sinensis

by Zhuo Yang, Wenli Mei, Hao Wang, Jun Zeng, Haofu Dai and Xupo Ding

Int. J. Mol. Sci. 2023, 24(24), 17384; https://doi.org/10.3390/ijms242417384 - 12 Dec 2023

Cited by 3 | Viewed by 721

Abstract

NAC is a class of plant-specific transcription factors that are widely involved in the growth, development and (a)biotic stress response of plants. However, their molecular evolution has not been extensively studied in Malvales, especially in Aquilaria sinensis, a commercial and horticultural crop that produces an aromatic resin named agarwood. In this study, 1502 members of the NAC gene family were identified from the genomes of nine species from Malvales and three model plants. The macroevolutionary analysis revealed that whole genome duplication (WGD) and dispersed duplication (DSD) have shaped the current architectural structure of NAC gene families in Malvales plants. Then, 111 NAC genes were systemically characterized in A. sinensis. The phylogenetic analysis suggests that NAC genes in A. sinensis can be classified into 16 known clusters and four new subfamilies, with each subfamily presenting similar gene structures and conserved motifs. RNA-seq analysis showed that AsNACs presents a broad transcriptional response to the agarwood inducer. The expression patterns of 15 AsNACs in A. sinensis after injury treatment indicated that AsNAC019 and AsNAC098 were positively correlated with the expression patterns of four polyketide synthase (PKS) genes. Additionally, AsNAC019 and AsNAC098 were also found to bind with the AsPKS07 promoter and activate its transcription. This comprehensive analysis provides valuable insights into the molecular evolution of the NAC gene family in Malvales plants and highlights the potential mechanisms of AsNACs for regulating secondary metabolite biosynthesis in A. sinensis, especially for the biosynthesis of 2-(2-phenyl) chromones in agarwood. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0)

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18 pages, 4583 KiB

Open AccessArticle

Molecular Regulatory Mechanism of Exogenous Hydrogen Sulfide in Alleviating Low-Temperature Stress in Pepper Seedlings

by Xueping Song, Li Zhu, Dong Wang, Le Liang, Jiachang Xiao, Wen Tang, Minghui Xie, Zhao Zhao, Yunsong Lai, Bo Sun, Yi Tang and Huanxiu Li

Int. J. Mol. Sci. 2023, 24(22), 16337; https://doi.org/10.3390/ijms242216337 - 15 Nov 2023

Cited by 1 | Viewed by 892

Abstract

Pepper (Capsicum annuum L.) is sensitive to low temperatures, with low-temperature stress affecting its plant growth, yield, and quality. In this study, we analyzed the effects of exogenous hydrogen sulfide (H₂S) on pepper seedlings subjected to low-temperature stress. Exogenous H₂S increased the content of endogenous H₂S and its synthetase activity, enhanced the antioxidant capacity of membrane lipids, and protected the integrity of the membrane system. Exogenous H₂S also promoted the Calvin cycle to protect the integrity of photosynthetic organs; enhanced the photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and photosynthesis; and reduced the intercellular CO₂ concentration (Ci). Moreover, the activities of superoxide dismutase, peroxidase, catalase, and anti-cyclic glutathione (ASA-GSH) oxidase were improved to decompose excess reactive oxygen species (ROS), enhance the oxidative stress and detoxification ability of pepper seedlings, and improve the resistance to low-temperature chilling injury in ‘Long Yun2’ pepper seedlings. In addition, the H₂S scavenger hypotaurine (HT) aggravated the ROS imbalance by reducing the endogenous H₂S content, partially eliminating the beneficial effects of H₂S on the oxidative stress and antioxidant defense system, indicating that H₂S can effectively alleviate the damage of low temperature on pepper seedlings. The results of transcriptome analysis showed that H₂S could induce the MAPK-signaling pathway and plant hormone signal transduction; upregulate the expression of transcription factors WRKY22 and PTI6; induce defense genes; and activate the ethylene and gibberellin synthesis receptors ERF1, GDI2, and DELLA, enhancing the resistance to low-temperature chilling injury of pepper seedlings. The plant–pathogen interaction was also significantly enriched, suggesting that exogenous H₂S also promotes the expression of genes related to plant–pathogen interaction. The results of this study provide novel insights into the molecular mechanisms and genetic modifications of H₂S that mitigate the hypothermic response. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0)

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19 pages, 9142 KiB

Open AccessArticle

Artificial Light for Improving Tomato Recovery Following Grafting: Transcriptome and Physiological Analyses

by Xiaotao Ding, Chen Miao, Rongguang Li, Lizhong He, Hongmei Zhang, Haijun Jin, Jiawei Cui, Hong Wang, Yongxue Zhang, Panling Lu, Jun Zou, Jizhu Yu, Yuping Jiang and Qiang Zhou

Int. J. Mol. Sci. 2023, 24(21), 15928; https://doi.org/10.3390/ijms242115928 - 03 Nov 2023

Viewed by 847

Abstract

Grafting is widely used to enhance the phenotypic traits of tomatoes, alleviate biotic and abiotic stresses, and control soil-borne diseases of the scion in greenhouse production. There are many factors that affect the healing and acclimatization stages of seedlings after grafting. However, the role of light has rarely been studied. In this study, we compared the effects of artificial light and traditional shading (under shaded plastic-covered tunnels) on the recovery of grafted tomato seedlings. The results show that the grafted tomato seedlings recovered using artificial light had a higher healthy index, leaf chlorophyll content, shoot dry weight, and net photosynthetic rate (P_n) and water use efficiency (WUE) compared with grafted seedling recovered using the traditional shading method. Transcriptome analysis showed that the differentially expressed genes (DEGs) of grafted seedlings restored using artificial light were mainly enriched in the pathways corresponding to plant hormone signal transduction. In addition, we measured the endogenous hormone content of grafted tomato seedlings. The results show that the contents of salicylic acid (SA) and kinetin (Kin) were significantly increased, and the contents of indoleacetic acid (IAA) and jasmonic acid (JA) were decreased in artificial-light-restored grafted tomato seedlings compared with those under shading treatments. Therefore, we suggest that artificial light affects the morphogenesis and photosynthetic efficiency of grafted tomato seedlings, and it can improve the performance of tomato seedlings during grafting recovery by regulating endogenous hormone levels. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0)

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16 pages, 8969 KiB

Open AccessArticle

Comparative Analysis of the Complete Mitochondrial Genomes of Apium graveolens and Apium leptophyllum Provide Insights into Evolution and Phylogeny Relationships

by Xiaoyan Li, Mengyao Li, Weilong Li, Jin Zhou, Qiuju Han, Wei Lu, Qin Luo, Shunhua Zhu, Aisheng Xiong, Guofei Tan and Yangxia Zheng

Int. J. Mol. Sci. 2023, 24(19), 14615; https://doi.org/10.3390/ijms241914615 - 27 Sep 2023

Viewed by 840

Abstract

The genus Apium, belonging to the family Apiaceae, comprises roughly 20 species. Only two species, Apium graveolens and Apium leptophyllum, are available in China and are both rich in nutrients and have favorable medicinal properties. However, the lack of genomic data has severely constrained the study of genetics and evolution in Apium plants. In this study, Illumina NovaSeq 6000 and Nanopore sequencing platforms were employed to identify the mitochondrial genomes of A. graveolens and A. leptophyllum. The complete lengths of the mitochondrial genomes of A. graveolens and A. leptophyllum were 263,017 bp and 260,164 bp, respectively, and contained 39 and 36 protein-coding genes, five and six rRNA genes, and 19 and 20 tRNA genes. Consistent with most angiosperms, both A. graveolens and A. leptophyllum showed a preference for codons encoding leucine (Leu). In the mitochondrial genome of A. graveolens, 335 SSRs were detected, which is higher than the 196 SSRs found in the mitochondrial genome of A. leptophyllum. Studies have shown that the most common RNA editing type is C-to-U, but, in our study, both A. graveolens and A. leptophyllum exhibited the U-C editing type. Furthermore, the transfer of the mitochondrial genomes of A. graveolens and A. leptophyllum into the chloroplast genomes revealed homologous sequences, accounting for 8.14% and 4.89% of the mitochondrial genome, respectively. Lastly, in comparing the mitochondrial genomes of 29 species, it was found that A. graveolens, A. leptophyllum, and Daucus carota form a sister group with a support rate of 100%. Overall, this investigation furnishes extensive insights into the mitochondrial genomes of A. graveolens and A. leptophyllum, thereby enhancing comprehension of the traits and evolutionary patterns within the Apium genus. Additionally, it offers supplementary data for evolutionary and comparative genomic analyses of other species within the Apiaceae family. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0)

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12 pages, 3122 KiB

Open AccessArticle

Comparative Transcriptome Analysis of Purple and Green Flowering Chinese Cabbage and Functional Analyses of BrMYB114 Gene

by Mei Fu, Juxian Guo, Kang Tang, Shizheng Jiang, Shanwei Luo, Wenlong Luo, Imran Khan and Guihua Li

Int. J. Mol. Sci. 2023, 24(18), 13951; https://doi.org/10.3390/ijms241813951 - 11 Sep 2023

Cited by 1 | Viewed by 875

Abstract

Flowering Chinese cabbage (Brassica rapa var. parachinensis) is one of the most popular vegetables in the south of China. As an antioxidant, anthocyanin is an important quality trait in vegetables, and the gene related to anthocyanin biosynthesis in purple flowering Chinese cabbage is also important. In this study, two flowering Chinese cabbage with extreme colors in the stem were used as materials for transcriptome analysis. RNA-seq analysis showed that 6811 differentially expressed genes (DEGs) were identified, including 295 transcription factors. Phenylpropanoid biosynthesis, flavone and flavanol biosynthesis, and flavonoid biosynthesis pathways were found to be significantly enriched in the purple flowering Chinese cabbage. A total of 25 DEGs associated with anthocyanin biosynthesis were found at a higher expression in purple flowering Chinese cabbage than in green flowering Chinese cabbage. Bioinformatics analysis shows that BrMYB114 is a candidate gene for the regulation of anthocyanin biosynthesis, and heterologous expression analysis of BrMYB114 in Nicotiana benthamiana indicates that BrMYB114 functions in anthocyanin biosynthesis. Therefore, our findings provide vital evidence for elucidating the molecular mechanism in the purple stem in flowering Chinese cabbage. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0)

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13 pages, 4301 KiB

Open AccessArticle

Effects of sgRNAs, Promoters, and Explants on the Gene Editing Efficiency of the CRISPR/Cas9 System in Chinese Kale

by Wenli Huang, Aihong Zheng, Huanhuan Huang, Zhifeng Chen, Jie Ma, Xiangxiang Li, Qiannan Liang, Ling Li, Ruobin Liu, Zhi Huang, Yaoguo Qin, Yi Tang, Huanxiu Li, Fen Zhang, Qiaomei Wang and Bo Sun

Int. J. Mol. Sci. 2023, 24(17), 13241; https://doi.org/10.3390/ijms241713241 - 26 Aug 2023

Viewed by 1023

Abstract

The CRISPR/Cas9 system is extensively used for plant gene editing. This study developed an efficient CRISPR/Cas9 system for Chinese kale using multiple sgRNAs and two promoters to create various CRISPR/Cas9 vectors. These vectors targeted BoaZDS and BoaCRTISO in Chinese kale protoplasts and cotyledons. Transient transformation of Chinese kale protoplasts was assessed for editing efficiency at three BoaZDS sites. Notably, sgRNA: Z2 achieved the highest efficiency (90%). Efficiency reached 100% when two sgRNAs targeted BoaZDS with a deletion of a large fragment (576 bp) between them. However, simultaneous targeting of BoaZDS and BoaCRTISO yielded lower efficiency. Transformation of cotyledons led to Chinese kale mutants with albino phenotypes for boazds mutants and orange-mottled phenotypes for boacrtiso mutants. The mutation efficiency of 35S-CRISPR/Cas9 (92.59%) exceeded YAO-CRISPR/Cas9 (70.97%) in protoplasts, and YAO-CRISPR/Cas9 (96.49%) surpassed 35S-CRISPR/Cas9 (58%) in cotyledons. These findings introduce a strategy for enhancing CRISPR/Cas9 editing efficiency in Chinese kale. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0)

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16 pages, 7806 KiB

Open AccessArticle

Genome-Wide Analysis of the MADS-box Gene Family and Expression Analysis during Anther Development in Salvia miltiorrhiza

by Songyue Chai, Kexin Li, Xuexue Deng, Long Wang, Yuanyuan Jiang, Jinqiu Liao, Ruiwu Yang and Li Zhang

Int. J. Mol. Sci. 2023, 24(13), 10937; https://doi.org/10.3390/ijms241310937 - 30 Jun 2023

Cited by 1 | Viewed by 1124

Abstract

MADS-box genes constitute a large family of transcription factors that play important roles in plant growth and development. However, our understanding of MADS-box genes involved in anther development and male sterility in Salvia miltiorrhiza is still limited. In this study, 63 MADS-box genes were identified from the genome of the male sterility ecotype Sichuan S. miltiorrhiza (S. miltiorrhiza_SC) unevenly distributed among eight chromosomes. Phylogenetic analysis classified them into two types and 17 subfamilies. They contained 1 to 12 exons and 10 conserved motifs. Evolution analysis showed that segmental duplication was the main force for the expansion of the SmMADS gene family, and duplication gene pairs were under purifying selection. Cis-acting elements analysis demonstrated that the promoter of SmMADS genes contain numerous elements associated with plant growth and development, plant hormones, and stress response. RNA-seq showed that the expression levels of B-class and C-class SmMADS genes were highly expressed during anther development, with SmMADS11 likely playing an important role in regulating anther development and male fertility in S. miltiorrhiza_SC. Overall, this study provides a comprehensive analysis of the MADS-box gene family in S. miltiorrhiza, shedding light on their potential role in anther development and male sterility. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0)

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13 pages, 11128 KiB

Open AccessArticle

Sequencing and Analysis of Complete Chloroplast Genomes Provide Insight into the Evolution and Phylogeny of Chinese Kale (Brassica oleracea var. alboglabra)

by Yilin Wang, Qiannan Liang, Chenlu Zhang, Huanhuan Huang, Hao He, Mengyu Wang, Mengyao Li, Zhi Huang, Yi Tang, Qing Chen, Huiying Miao, Huanxiu Li, Fen Zhang, Qiaomei Wang and Bo Sun

Int. J. Mol. Sci. 2023, 24(12), 10287; https://doi.org/10.3390/ijms241210287 - 17 Jun 2023

Cited by 3 | Viewed by 1530

Abstract

Chinese kale is a widely cultivated plant in the genus Brassica in the family Brassicaceae. The origin of Brassica has been studied extensively, but the origin of Chinese kale remains unclear. In contrast to Brassica oleracea, which originated in the Mediterranean region, Chinese kale originated in southern China. The chloroplast genome is often used for phylogenetic analysis because of its high conservatism. Fifteen pairs of universal primers were used to amplify the chloroplast genomes of white-flower Chinese kale (Brassica oleracea var. alboglabra cv. Sijicutiao (SJCT)) and yellow-flower Chinese kale (Brassica oleracea var. alboglabra cv. Fuzhouhuanghua (FZHH)) via PCR. The lengths of the chloroplast genomes were 153,365 bp (SJCT) and 153,420 bp (FZHH) and both contained 87 protein-coding genes and eight rRNA genes. There were 36 tRNA genes in SJCT and 35 tRNA genes in FZHH. The chloroplast genomes of both Chinese kale varieties, along with eight other Brassicaceae, were analyzed. Simple sequence repeats, long repeats, and variable regions of DNA barcodes were identified. An analysis of inverted repeat boundaries, relative synonymous codon usage, and synteny revealed high similarity among the ten species, albeit the slight differences that were observed. The Ka/Ks ratios and phylogenetic analysis suggest that Chinese kale is a variant of B. oleracea. The phylogenetic tree shows that both Chinese kale varieties and B. oleracea var. oleracea were clustered in a single group. The results of this study suggest that white and yellow flower Chinese kale comprise a monophyletic group and that their differences in flower color arose late in the process of artificial cultivation. Our results also provide data that will aid future research on genetics, evolution, and germplasm resources of Brassicaceae. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0)

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Review

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22 pages, 4482 KiB

Open AccessReview

Recent Advances in Tomato Gene Editing

by Eduardo Larriba, Olha Yaroshko and José Manuel Pérez-Pérez

Int. J. Mol. Sci. 2024, 25(5), 2606; https://doi.org/10.3390/ijms25052606 - 23 Feb 2024

Viewed by 1520

Abstract

The use of gene-editing tools, such as zinc finger nucleases, TALEN, and CRISPR/Cas, allows for the modification of physiological, morphological, and other characteristics in a wide range of crops to mitigate the negative effects of stress caused by anthropogenic climate change or biotic stresses. Importantly, these tools have the potential to improve crop resilience and increase yields in response to challenging environmental conditions. This review provides an overview of gene-editing techniques used in plants, focusing on the cultivated tomatoes. Several dozen genes that have been successfully edited with the CRISPR/Cas system were selected for inclusion to illustrate the possibilities of this technology in improving fruit yield and quality, tolerance to pathogens, or responses to drought and soil salinity, among other factors. Examples are also given of how the domestication of wild species can be accelerated using CRISPR/Cas to generate new crops that are better adapted to the new climatic situation or suited to use in indoor agriculture. Full article

(This article belongs to the Special Issue Horticultural Crop Improvement: A New Era for Plant Molecular Research 2.0)

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